Innate Immune System Composition

The main functions of the innate immune system include (1) the clearance of foreign and potentially detrimental self-materials through the recruitment, activation, and effector activity of immune cells; (2) activation of the complement pathways, and (3) triggering of the adaptive immune response (see also Chapter 18). A key feature of the innate, and to some extent the adaptive, immune system is that it is activated by the engagement of pattern-recognition receptors (PRRs) that recognize common structures on pathogens and also a few self-molecules such as certain damage-associated molecular patterns (DAMPs) (e.g., heat shock proteins),³³ released during cellular stress, injury, or death. PRRs can be classified by their location into secreted, transmembrane, or cytosolic types.³¹ Secreted PRRs include collectins, pentraxins, ficolins, and to some extent C1q, properdin, serum amyloid A, and mindin, which facilitate clearance of pathogens by promoting opsonization and complement activation.³⁴ Transmembrane PRRs that provide activating signals following engagement with the corresponding PAMPs include the Toll-like receptors (TLRs), several C-type lectin receptors (dectin receptors, mannose receptor, DC-SIGN), and N-formyl methionine receptors.³⁵

The TLRs are of particular interest because of their role in autoimmune diseases such as SLE.³⁶ They are a family of type I membrane proteins that contain a ligand-binding ectodomain composed of 18 to 25 tandem leucine-rich repeats, a transmembrane region, and an intracellular cytoplasmic Toll/interleukin 1 receptor (TIR) domain through which they interact with two main adapters, MyD88 (all TLRs except TLR3) and TRIF (TLR3, TLR4).^37,38 TLRs are either expressed as cell surface receptors where they recognize primarily bacterial products such as lipoteichoic acids (TLR1/2 heterodimer), lipoproteins (TLR2/6), lipopolysaccharide (TLR4), and flagellin (TLR5), or in the endolysosomal compartment where they bind different types of nucleic acids including dsRNA (TLR3), ssRNA (TLR7), and dsDNA (TLR9). The intracellular location of the nucleic acid–binding TLRs is thought to reflect both the optimal location for exposure to microbial nucleic acids, which are released in the endolysosomes following phagocytosis, and the necessity of avoiding activation by extracellular self-nucleic acids.³¹ Cell types express different combinations of TLR members, reflecting the role of specific TLRs in cell function (e.g., the endosomal TLRs recognizing nucleic acids are predominantly expressed in phagocytes and antigen-presenting cells).

The cytosolic PRRs include (1) RIG-I-like receptors (RLRs) that include RIG-I, a sensor for foreign uncapped 5′-triphosphate RNA and MDA5 that recognizes long dsRNA^39,40; (2) NOD-like receptors (NLRs) that recognize bacterial cell wall products^41,42; and (3) several DNA sensors, IFI16,^43,44 LRRFIP1,⁴⁵ Ku70,⁴⁶ AIM2, and DNA-dependent RNA polymerase III, which does not detect DNA directly but transcribes AT-rich DNA to 5′uncapped 5′-triphosphate RNA that in turn activates RIG-I.^7,32,47,48 The role of these cytosolic PRRs in autoimmune diseases has not yet been defined.⁴⁹

Collectively, engagement of the TLR and cytosolic PRRs activates immune cells through several signaling pathways that converge primarily to activate nuclear factor κB (NFκB)/cytokine or inflammasome programs. Furthermore, depending on the PRRs engaged, cell types activated, and site of activation, this system of receptors facilitates the generation of nuanced responses to a wide array of potential pathogens.⁵⁰

Major innate immune system cell types include macrophages, dendritic cells, neutrophils, plasmacytoid dendritic cells (pDC), natural killer (NK) cells, basophils, mast cells, and eosinophils. In addition, certain T lymphocyte subsets that express predominantly invariant antigen receptors that recognize microbial products such as certain γδ-T cells⁵¹ and NK T cells⁵² might also be considered part of the innate system. Similarly, certain B lymphocyte subsets, including B1 and marginal zone B cells, have characteristics suggesting a lineage with innate properties (e.g., development from precursors early, but not late in life, the capacity for self-renewal and expression of primarily low-affinity polyreactive IgM).

The innate response is also strongly influenced by nonhematopoietic cells including endothelial, stromal, fibroblast, and keratin cells that can elaborate proinflammatory factors following engagement of PRRs, injury, or activation by the adaptive immune system. Examples include, nonhematopoietic cells are required for NOD 1 receptor-mediated Th2 immune responses⁵³, synovial fibroblasts play a central role in RA⁵⁴, and keratinocyte secretion of CSF-1 after UV exposure promotes cutaneous lupus.⁵⁵

The complement system⁵⁶ comprises an immune surveillance system that interacts with, and promotes elimination of, modified host cells, cellular debris, and foreign entities (see also Chapter 23). This system is tightly interconnected with inflammatory, immune, and other pathways and because of this, often plays important roles in both autoinflammatory and autoimmune diseases.

Activation of the complement cascade occurs through the classical, alternative, and lectin pathways, which function in complement-mediated lysis (C5b-C9 attack complex), release of proinflammatory mediators (C3a, C5a), opsonization (C1q, mannose binding lectin), and B cell activation (iC3b, C3dg; activation of B cells via CR2). Complement is regulated by soluble factors (C1 esterase inhibitor, sMAP and MAP-1, C2 receptor inhibitor trispanning, factor H, factor H-like protein 1, and C4b-binding protein), as well as cell surface decay accelerators such as CR1 and DAF (CD55), inhibitors of the terminal complement complex (CD59, vitronectin, clusterin), carboxypeptidase-N, and CD46. Major functions are the killing and elimination of pathogens, initiation and amplification of inflammation, safe removal of apoptotic cells and material, interaction with TLR signaling and coagulation pathways, and in facilitating immune complex clearance, angiogenesis, and tissue regeneration. Importantly, complement enhances and modulates humoral and cellular immune responses by several mechanisms including C3dg opsonization of antigen that promotes both costimulation of B cells via complement receptor 2 (CR2) binding and the capture of antigen on follicular DC (FDC) by CR1/2; activation of the C5aR on immune cells; along with direct and indirect effects of complement components on T cell activation and differentiation.

Adaptive Immune System Composition

The main constituents that distinguish the adaptive from the innate immune response are the B and T lymphocytes, which express an expansive array of diverse antigen receptors (see also Chapter 19). In aggregate, the pool of lymphocytes is capable of recognizing virtually all antigens and, by the process of selection, lymphocytes with beneficial specificities can be expanded and retained. These properties allow the immune system to detect a manifold galaxy of foreign antigens and to respond rapidly and specifically to secondary challenges. T and B lymphocyte antigen receptors are created by the random recombination of a large number of variable region (V-D-J) gene segments and diversity-producing end-joining mechanisms in primary lymphoid organs. Furthermore, peripheral B cells can also increase specificity by somatic hypermutation and selection of higher affinity clones. The clonal nature of lymphocytes, bestowed by uniquely rearranged antigen receptors, is key to the exquisite discriminating power of the immune system. Clonality also extends to other characteristics such as cytokine production, surface receptors, and cell signaling molecules.

T cells play a central role in the adaptive immune response through elaboration of cytokines such as IFN-γ and TNF, IL-4, and IL-17, by providing essential signals to B cells in T cell–dependent humoral responses, as direct killers of cells, and by promoting inflammation in target tissues (see also Chapter 13). Importantly, because of their clonal nature and the immune system’s ability to neutralize specific self-reactive clones, they play a fundamental role in regulating autoreactivity. T cells arise in the thymus, where they transit through defined maturation stages and undergo positive and negative clonal selection.^57,58 Thymic-derived T cell populations include the classical CD8 and CD4 αβ T cells, γδ T cells, NK T cells, natural regulatory CD4 T cells (nTreg), and a subset of NK cells.⁵⁹ Recent thymic CD4 and CD8 T cell emigrants mature in the periphery, where, unless activated, they can remain as circulating naïve T cells for the lifespan of the organism. Following activation by antigen-presenting cells, T cells expand and differentiate into several possible subsets. For CD4 T cells, these include the major Th1, Th2, Th17, follicular helper (Tfh), induced Treg (iTreg) subsets, and the less well-defined Th9 and Th22 populations that promote or inhibit distinct immune response activities.^60–62

B cells develop in the bone marrow, where, like T cells, they undergo defined maturation stages and selection of antigen receptors (see also Chapter 14). In addition, class-switch recombination and somatic hypermutation of the B cell receptor occurs during T cell–dependent humoral responses. The main B cell types in the periphery include the conventional (or B2) and B1 subsets, with B2 cells further divided into follicular and marginal zone subsets.

Other essential constituents of the adaptive immune system are the professional antigen-presenting cells including, in addition to B cells, conventional dendritic cells (cDCs) and macrophages. Several other cell populations also directly affect adaptive immunity and include the follicular DCs, stromal cells, thymic epithelial cells, and others, while cell types such as NK cells, NK T cells, mast cells, and basophils variously modify adaptive responses.

Clone-Specific Self-Nonself Recognition

In contrast to innate immune cells, which are activated primarily by hardwired microbial PRRs, lymphocytes are unrestricted in specificity and therefore self-nonself discrimination must be implemented at the clonal level. To achieve this, T and B cells use several mechanisms that can be grouped into three general strategies. First, the type of response is controlled by developmental stage. For example, immature lymphocytes respond to strong antigen receptor stimulation by cell death, whereas a similar signal in mature cells leads to activation. Through this mechanism self-reactive clones are eliminated from the nascent lymphocyte repertoire before they can cause injury. Second, activation of mature lymphocytes requires—in addition to antigen receptor engagement—a second co-stmulatory signal that, if absent, results in anergy or cell death. For the most part, this requirement limits reactivity to self because co-stimulatory signals are largely provided by activated cells of the innate immune system. Third, lymphocytes are fine-tuned in various ways by a fairly extensive list of modulating factors, which is necessary for controlling self-reactive clones.^70–72 For example, defects affecting a broad range of surface receptors on lymphocytes, including those with prosurvival (IL-7R, BAFFR, IL-2R); proapoptotic (TNFRs, FasL, TRAIL); costimulatory (CD28, CD40, TLRs); differentiating (IL-12R, IL-4R, IFNγR, IL-23R, retinoic acid R, transforming growth factor (TGF)-βRs, SAP/SLAM family members, OX40, ICOS/ICOSL); inhibitory (FcγRIIb, CD22, CTLA4, PD-1); antigen receptor signal modulating (CD19, CD45); and activating (SAP/SLAM family members) activities have been shown to influence the development of autoimmunity.⁹ Collectively, these self-nonself recognition mechanisms provide the basic cellular means by which the innate and adaptive immune systems render T and B cell clonotypes tolerant to self-antigens and resistant to autoimmune disease.

Innate System and Tolerance

Given its vital role in initiating and modulating adaptive immune responses, it is not surprising that the innate immune system strongly influences both tolerance and autoimmunity. Indeed, although its contributions have yet to be fully explicated, several ways in which self-tolerance is influenced by the innate arm have been defined. First, as noted previously, activation of the innate immune system under normal circumstances typically requires engagement of microbial PRRs, which endows the immune system with a direct and simple way to distinguish foreign- from self-antigens.⁷³ The importance of this mechanism is illustrated by the finding that overexpression of TLR7 by spontaneous gene duplication or transgenic approaches promotes systemic autoimmunity.³⁶ This occurs because certain PRRs, such as TLR7 and TLR9 that equally sense both foreign and self-nucleic acids, avoid significant exposure to endogenous nucleic acids by virtue of their location in subcellular compartments.⁷⁴ However, in the case of TLR7, overexpression makes it possible for normally substimulatory amounts of endogenous RNA to activate immune cells, thereby bypassing the usual requirement for microbial exposure. Second, some cells of the innate immune system actively suppress adaptive immune system activation under certain conditions. For example, immature and, under some circumstances, even mature dendritic cells have been shown to promote tolerance by inducing CD4 T regulatory (Treg) cells and other mechanisms.⁷⁵ Third, another critical function of the innate immune system is the rapid noninflammatory clearance of apoptotic cells.⁷⁶ Failure can result in an increased supply of self-antigenic material including nucleic acids, secondary necrosis, and release of proinflammatory factors, leading to systemic autoimmunity.⁷⁷ Accordingly, deficiencies in several key apoptotic cell clearance molecules are associated with autoimmunity including (1) the Tyro3-Axl-Mer receptors on phagocytes that bind through Gas6 or protein S, the exposed phosphatidylserine (PS) on apoptotic cells⁷⁸; (2) the milk fat globule-EGF factor 8 (MFG-E8) protein that bridges the αvβ3 integrin on phagocytes and PS on apoptotic cells^79,80; and (3) natural IgM or C1q that binds to and enhances clearance of apoptotic cells.^81–83 Fourth, several complement components have been directly implicated in autoimmunity. For example, SLE is associated with deficiencies of proximal components of the classical pathway including C1q, C4, and C2. The mechanism for this is not certain, but both defective clearance of apoptotic material/immune complexes and a shift in the activation threshold of lymphocytes have been suggested.⁸⁴ As another example, deficiency of CD55 (or decay-accelerating factor), a cell surface protein that restricts complement activation, is associated with enhanced T cell responses and exacerbation of neuroinflammation and lupus in animal models.^85,86 Thus at many levels, the innate immune system plays a critical role in maintaining tolerance and controlling autoimmunity.

T Cell Tolerance

T cells are critical players in both achieving and fine-tuning tolerance to a high degree of specificity. Researchers have identified several mechanisms and divided them into three main areas: central tolerance wherein T cells first acquire their antigen receptor, peripheral tolerance wherein T cells encounter self-antigens not present in the thymus, and postactivation regulation wherein activated and expanded T cell clones are returned to their resting state. Central tolerance, as alluded to earlier, is imposed on T cells with self-reactive specificities during thymocyte development by mechanisms using primarily deletion, to a lesser extent anergy, and possibly receptor editing of the TCR α-chain.^87,88 This process, although highly effective, is not completely efficient, and T cells with autoreactivity, primarily those with intermediate to low affinity to self or recognizing self-antigens poorly expressed in the thymus, emigrate in significant numbers. This leakiness is probably necessary to generate a broad repertoire, but it then creates vulnerability to autoimmunity and necessitates peripheral tolerance mechanisms.

In the periphery, multiple mechanisms for avoiding autoreactivity have been identified. Among these, a common explanation is that most tissue-associated self-antigens are not accessible to trigger a response, a situation that can be caused by low abundance, specific characteristics of the self-antigen, or location. This mechanism is supported experimentally by the finding that T cells expressing a transgenic TCR to certain tissue-specific antigens are not deleted or activated, nor do they cause autoimmune disease. Yet these so-called “ignorant” T cells are fully functional and respond to self-antigen when presented in a conventional context such as inflammation or tissue damage.^18,89 For a few self-antigens such as those expressed in the anterior chamber of the eye, central nervous system, or other so-called immunologic privileged sites—as originally defined by their ability to accept allograft transplants—resistance to self-reactivity also partly arises from anatomic sequestration caused by limited access of blood-borne cells and the absence of conventional lymphatic drainage.⁹⁰ The latter is important because T cells are typically first activated in secondary lymphoid organs and subsequently migrate to target organs, where reactivation by local antigen-presenting cells and the production of proinflammatory factors leads to tissue damage.⁹¹ Anatomic sequestration alone, however, is not sufficient for tissues to support immunologic privilege and, as discussed later, such sites employ a host of additional local mechanisms.^92,93

Another peripheral mechanism is the aforementioned two-signal paradigm wherein T cell activation requires both TCR engagement and a co-stimulatory signal usually provided by CD28. Because the two ligands for CD28, CD80 and CD86, are primarily expressed at high levels on activated professional antigen-presenting cells, presentation of self-antigen by quiescent antigen-presenting cells would lead to tolerance. Indeed, immature DCs promote tolerance in this manner by constitutively presenting low doses of self-antigen on MHC, resulting in cell death or anergy of the corresponding T cells.⁹⁴

Peripheral tolerance of T cells is also maintained by active suppression via immunoregulatory cells of the immune system, among which CD4⁺ Tregs are the best characterized. They constitute a distinct αβ T cell subset generated in the thymus (natural Treg, nTreg) or in the periphery from naïve or mature CD4⁺ T cells exposed to TGF-β (induced Treg, iTreg). Both are developmentally induced by the Foxp3 (forkhead boxP3) transcription factor. They typically express high levels of the IL-2 receptor component, IL-2Rα (CD25), and require IL-2 for survival. Tregs participate in every adaptive immune response, are critical for maintaining the proper level of immune response, and are activated at the same time as conventional T cells. They are thought to suppress the magnitude of the response by (1) initially downregulating DC function and then inhibiting T cell activation by competing for IL-2, (2) producing immunosuppressive cytokines such as TGF-β, IL-10, and IL-35, and (3) by cell-cell inhibitory interactions that lead to cell killing or the induction of negative signals.⁹⁵ These inhibitory actions suppress T cells that are in proximity to Treg cells regardless of their antigen specificity.⁹⁶ Researchers have described other T cells with regulatory activity in autoimmunity including Tr1, CD8 Treg, Qa-1/HLA-E-restricted CD8 T cells, and γδ T cells, but they are less well characterized.^97–101

Tissues themselves also employ mechanisms that suppress self-reactivity and contribute to establishing immune privilege.^92,102–104 These comprise three general categories. First, certain tissues are decorated with cell surface inhibitory molecules such as the proapoptotic FasL and TRAIL, lymphocyte inhibitory and Treg-promoting PD-L2, and complement regulatory proteins, CD55 and CD46, that can potentially eliminate or impede the activation of autoreactive T cells. Second, soluble inhibitors of inflammation and immune activation are secreted by particular tissues. Notably, in the aqueous humor of the eye, there is a broad spectrum of such factors that include TGF-β, α-melanocyte-stimulating hormone, vasointestinal peptide, calcitonin gene–related peptide, somatostatin, macrophage inhibitory factor, and complement inhibitors. Third, lymph node resident stromal cells have been shown to induce tolerance of CD8⁺ T cells recognizing peripheral tissue-restricted self-antigens.^105,106 Thus, it has been proposed that stromal cells in lymph node and tissues may provide a means to eliminate T cells that bind to tissue-restricted antigens not expressed in the thymus. Fourth, the anterior chamber of the eye elicits a unique type of altered immune response through a complex multistep process termed anterior chamber-associated immune deviation (ACAID) that leads to a dampened and less tissue-destructive response.^92,104,107 Although ACAID was long thought important for tolerance, it was recently argued that its primary function may be to modulate the immune response so that the eye can respond to infection without damaging its integrity.¹⁰⁸

Another possible peripheral mechanism is immune deviation wherein polarization away from a predisposing cytokine pattern, such as from a Th1 to a Th2 profile, suppresses the development of autoimmune disease.¹⁰⁹ Similarly, activation of NKT cells with α-GalCer, which induces IFN-γ production, is associated with dampening of the adaptive Th1 and Th17 effector responses and protection from experimental autoimmune uveitis.¹¹⁰ In these models, autoreactive T cells are activated but do not produce the proinflammatory factors necessary for tissue damage.

In addition to central and peripheral tolerance, the immune system must also avert autoimmunity by suppressing or eliminating T cells following their activation or expansion. This regulation is mediated by several processes, including upregulation of inhibitory receptors such as CLTA4, expression of proapoptotic receptors like Fas, and release of intracellular proapoptotic factors such as Bim. Deficiencies of such mediators that control the magnitude of T cell responses are associated with severe expansion of lymphocyte populations and with varying degrees of autoimmunity.

B Cell Tolerance

B cells are required not only for antibody production but also serve as potent antigen-presenting cells for T cells and follicular DCs, and can act in regulation as well.¹¹¹ Moreover, depletion of B cells with rituximab has shown promise even in autoimmune diseases considered to be mediated by T cells such as T1DM¹¹² and multiple sclerosis.¹¹³ Therefore, there is substantial interest in defining both mechanisms of B cell tolerance and the specific role of B cell tolerance in autoimmune disease.

Before discussing specific tolerance mechanisms, however, it should be emphasized that the fate of B cells after antigen receptor (BCR) cross-linking is highly dependent on developmental stage, context and strength of signal, and the nature of the antigen, probably more so than for T cells because B cells are subjected to less stringent selection during central tolerance. Several checkpoints considered important for controlling autoreactive B cells and for maintaining self-tolerance have been identified and include many central and peripheral mechanisms similar to those described for T cells, as well as a few additional ones.

Central tolerance of B cells takes place in the bone marrow during preB to immature B cell transition as they express rearranged immunoglobulin (Ig) genes on their surface.¹¹⁴ It appears that the dominant mechanism for B cells with high affinity to membrane-bound self-antigen is receptor editing (replacement of L-chain) and, to a lesser extent, deletion, while soluble self-antigens induce both receptor editing and anergy.^115,116 Anergic B cells are detectable in the periphery as an IgD⁺IgM⁻ population¹¹⁷ or in mice as splenic transitional 3 (T3) B cells.¹¹⁸ They are short-lived at least in part because they downregulate the BAFF receptor, which is required for their survival, putting them at a competitive disadvantage with other immature B cells, and they are less able to enter B cell follicles.

In the periphery, the earliest tolerance checkpoint occurs at the transitional 1 (T1) B stage over a 2-day interval before maturation to T2 and later naïve B cell subsets.^{114,119–121} T1 B cells are the immediate bone marrow emigrant population, retain an immature phenotype, and are BAFF-dependent for survival. Importantly, they undergo apoptosis and not activation when stimulated, which results in deletion of B cells recognizing peripheral self-antigens not expressed in the bone marrow compartment. Thus, this mechanism, which is unique to B cells, represents in essence an extension of central tolerance to the periphery.

Other peripheral tolerance mechanisms are achieved through many of those described earlier for T cells but differ qualitatively due to distinct differentiation pathways and differences in antigen recognition by B cells and T cells (i.e., BCRs can bind to virtually all tertiary structures while TCRs are restricted to recognizing self-MHC/peptide complexes on host cell surfaces). Accordingly, B cells can be ignorant of their corresponding self-antigen because of insufficient quantity or access¹⁹ or can undergo anergy and ultimately cell death if there is engagement of the BCR without co-stimulation (i.e., two signals).¹²²

Another notable checkpoint occurs during T cell–dependent immune responses as B cells undergo affinity maturation in germinal centers (GCs) and acquire new specificities, which may include self-reactivity. Evidence suggests that tolerance at this juncture is often defective in autoimmune diseases because most autoantibodies have acquired autoreactivity through somatic hypermutation and are class-switched,^123–125 both indicative of GC maturation. Although recent studies have provided significant insights into GC processes involved in the selection of B cell clones with high affinity to foreign antigens, how tolerance of class-switched autoreactive B cells is achieved remains to be clarified. Nevertheless, the strongest evidence suggests (1) autoreactive B cells compete poorly for the cognate T cell help essential for GC B cell survival because the autoreactive BCR would bind less well to the original antigen, resulting in less internalization of antigen for processing and presentation to T cells^126–128 and (2) B cells that acquire BCRs with high affinity to membrane antigens are deleted by a Fas-dependent mechanism.¹²⁹

Defective Tolerance

Although one can infer that loss of tolerance underlies autoimmunity, the specific tolerance defects causing common autoimmune diseases have been difficult to delineate, presumably because of modest defects at multiple checkpoints. Nevertheless, studies of monogenic human autoimmune disease and animal models have identified a wide range of defects in the various layers of central and peripheral tolerance. Such defects are caused by diverse genetic abnormalities and are mediated by a variety of lymphoid and nonlymphoid cell types. A few representative examples follow.

Defects in central tolerance have long been suspected to cause autoimmunity because of its well-documented role in eliminating nascent self-reactive lymphocytes, but until recently solid evidence for this was lacking. A breakthrough came from the discovery that mutations in a transcription factor, AIRE (for autoimmune regulator), caused autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED), a rare inherited disease associated with T cell and autoantibody–mediated autoimmune destruction of multiple endocrine organs.^130,131 AIRE-deficient mice developed a similar syndrome, which was caused by reduced expression of thousands of peripheral tissue genes in the thymic medullary epithelium and consequently failure to eliminate T cells specific for those gene products. Thus it appears that the main function of AIRE is to prevent autoimmunity by deleting T cells recognizing peripheral tissue self-antigens.

Another example of altered thymic selection leading to autoimmunity, but in this instance caused by a defect in T cells, is the aforementioned SKG arthritis model. Here, a function-impairing mutation in the C-terminal SH2 domain of ZAP-70, a Syk family tyrosine kinase activated by the T cell receptor complex ζ-chain, reduces TCR signaling, leading to defective conventional T cell and nTreg development in the thymus, and presumably enhanced positive selection of autoreactive T cells.¹³² Interestingly, using several ZAP-70 mutants, researchers showed that slight differences in ZAP-70-mediated signaling strength affected arthritis susceptibility.^132,133

For B cells, major defects in central tolerance leading to autoimmunity have been more difficult to prove and no AIRE-like equivalent has been discovered. Nevertheless, defective central tolerance of B cells in autoimmunity has been suggested by the finding of a higher frequency of naïve mature B cells with self-reactivity in patients with SLE and RA.^134–136

Moving to the periphery, an example of defective peripheral tolerance promoting autoimmunity is FAS deficiency.¹³⁷ FAS is a proapoptotic surface receptor that plays a critical role in maintaining immunologic homeostasis by eliminating undesired cells. Defects in FAS cause autoimmune lymphoproliferative syndrome (ALPS), also called Canale-Smith syndrome, and in mice, lymphoproliferative (lpr) disease, both of which exhibit massive enlargement of secondary lymphoid organs—caused mainly by the accumulation of a normally rare so-called “double negative” subset of T cells that lack both CD4 and CD8 co-receptors—and a variety of autoimmune manifestations. Lpr mice are defective in eliminating B cells that acquire self-reactivity in the periphery, a process that typically occurs in the GC during somatic hypermutation.¹²⁹ Similar abnormalities have been described in humans and mice with defects in the ligand for FAS, FASLG.¹³⁸

Peripheral tolerance is also breached by overexpression of the costimulatory molecule ICOS on T follicular helper (Tfh) cells in Sanroque mice. These mice have a point mutation in the Rc3h1 gene, a RING-type ubiquitin ligase, that impairs its ability to degrade ICOS mRNA.¹³⁹ Increased expression of ICOS promotes the expansion of Tfh cells and germinal centers, production of IL-21, and autoimmunity.¹⁴⁰

An example of a lymphocyte-extrinsic cause for loss of tolerance and autoimmunity is deficiency in the 3′ repair exonuclease 1 (TREX1, DNase III). Loss-of-function mutations in TREX1 have been implicated in the Aicardi-Goutières syndrome, a rare progressive encephalopathy associated with elevated IFN-α levels in cerebrospinal fluid, and chilblain lupus, a rare form of SLE characterized by painful, bluish-red inflammatory skin lesions typically affecting areas exposed to cold.^141,142 Autoimmunity is thought to be caused by the intracellular accumulation of ssDNA derived from endogenous retroelements normally degraded by TREX1, resulting in the activation of intracellular DNA sensors and consequent over production of IFN-α.^143,144 The importance of DNA disposal in lupus has been further illustrated by the association of DNase I deficiency with development of lupus in humans and mice.^145,146

Defective regulation can also result in loss of tolerance and autoimmune disease as illustrated by the absence of Tregs.^147,148 In humans, monogenic deficiency of the FOXP3 gene, which is required for Treg development, is associated with the IPEX (immune dysregulation, polyendocrinopathy, enteropathy X-linked) syndrome, a severe systemic autoimmune disease associated with diarrhea, eczematous dermatitis, and endocrinopathy, usually fatal within the first year. T1DM, autoimmune cytopenias, and nephritis are among other less common autoimmune manifestations of this syndrome. Similar findings are observed in scurfy mice that have a spontaneous function-impairing mutation of Foxp3.